Pokemon Special: Team Rocket's Last Stand
by Chaoticknight24
Summary: After two years of having defeated Kyogre in the Emerald Arc, peace has finally been returned to the Kanto Region! Or so we thought. Team Rocket has captured Red and it is up to the Pokedex holders to stop them.
1. Chapter 1a: The Attack in Viridian

Pokemon Adventures: Team Rocket's Last Stand

**_Chapter 1a: The Attack in Viridian Forest(Yellow POV)_**

The da y was bright and beautiful, and the Pidgey were simply flying through the sky, as if they appreciate the freedom given to them being flying types. There were no irregularities in the sky, only blue and gold as far as the eye. The Magikarp and the Goldeen jumping out of the water, as if seeming to taunt fishermen nearby. Ratata were chasing each other around the forest, protecting their nests from any danger that is approaching. People consider the beauty and tranquility of the Viridian Forest to be the greatest of them all.

This is my hometown's forest, where I go to think, play, and remember where it all began. My adventures began only because I was saved by Red that day. It was scary back then, because team rocket had enraged the pokemon and they had gone berserk. However, Red defeated Giovanni, and then all of the creatures of the viridian forest had calmed down. New populations were added to the Viridian Forest, however this only added more colors and texture to the forest further enhancing it's beauty.

How many times had this place been a battlefield for Team Rocket? How many people and pokemon had lost their lives to attempt to do the ridiculous things that Team Rocket set out to do? I don't even want to think about what would've happened if Red had not fought against Team Rocket. All of this peace is possible thanks to the effort of Red, Green, and Blue.

*_RING RING RING, RING RING RING PHONECALL, PHONECALL!* _The Pokegear that Professor Oak had given to me began to ring. At first, the Pokegear was only usable in the Johto Region due to technical limitations. That was until the genius creators and managers of the Pokemon Transfer System got their hands on it and fixed the device to work across Kanto and Johto.

"Hello, who is this?" I asked because I ignorantly forgot to check the id of the person calling. I'm such a klutz when it comes to this new technology.

"Yellow, I have captured Red, if you want him alive come to Saffron City by tomorrow at 9:00 pm. And let me tell you, we don't act nice to people who are late to our meetings." The voice answered as he hung up.

The voice had power and authority to it, however it wasn't Giovanni. I think it was Lt. Surge, because he is one of the only people I've met that actually scares me the same way Giovanni does. He told me to meet him at Saffron City, but I have no means of transportation to actually get there. Also, he said that he 'captured Red', what did he mean by capture? Couldn't he have easily said kidnapped? It would've made more sense.

Wait! I have to time to be thinking about things like this, first I have to find a way to get to Saffron City in one day. I looked down at my Pokegear and start looking through the contacts. I tried calling both Red and Blue but they wouldn't pick up. My only option left is to call Green, the current gym leader of Viridian City. He has a Charizard that can fly us over there and if Red is out of the count he is probably the only one who can rival Team Rocket's power.

"Come on...Please Pick up!" I said to myself as I heard the ringing noise for about ten seconds.

"...Hello? Yellow, what's up?' Green answered with his usual serious tone.

"Green! You picked up! Thank goodness!" After this introduction I explained the situation to him.

"I see, so Red's been taken hostage and you were told to go to Saffron City. You said you were in Viridian Forest right? I'll pick you up just wait about five minutes."

Suddenly, I started to hear heavy footsteps marching through the forest. It sounded like a single entity, but this one creature had the power to make the entire forest shake in fear. Judging from the footsteps, it was a beast with four legs on the ground. Although it sounds powerful it seems to be confused as the sound of his footsteps stops occasionally. A purple mist started to cover the air around me.

"This is sweet scent! It's trying to lure something out!"

I began to run, but the faster I ran the more frequently and the closer the footsteps behind me would get. It was moving quickly, and when I had turned around and decided to face it I saw a Venusaur. However, this wasn't an ordinary Venusaur; it had a blue flower on it's back, the skin was a night sky black, and it had red bloodshot eyes. Once the creature had seen me he had roared, not a roar that symbolizes he entered battle, but a cry of pain.

The Venusaur had used the powerful Frenzy Plant, and had destroyed all of the trees within a twenty feet radius of us. If I didn't bring out Kitty at the right moment I probably would've lost my life along with all of the poor trees in that forest. The Venasaur had roared again, his cry of pain. I can tell, this is Red's Venusaur, but why does it seem so different? Why is it in pain?

"Mr. Mime, use Psychic!" After hearing this, Butterfree and I had been slammed straight to the ground by a mysterious force. I looked up and saw a girl in a Team Rocket Uniform. With her long hair and her intimidating presence, I couldn't move because she was beautiful and intimidating. Yet I've met her before, and not in a situation like this.

"Yellow, although Lt. Surge should've told you to go to Saffron City, we were also told that we could exterminate you if we managed to get to you first. Go Venusaur, finish this foolish child off once and for all!"

No! This can't be the end! I haven't saved Red, I haven't even met up with Green yet! I can't die here! But I can't move because the Mr. Mime is still using it's Psychic attack on me. I'm pegged to the ground on my home turf unable to move! I heard the Venusaur's Roar once again, it seemed to be charging up it's Frenzy Plant. I can't dodge, it's over for me...

**Chapter 1a: The Sudden Threat(Silver POV)**

The town had it's usual annoying lights and noises, but I arrived here in Goldenrod city because Blue told me she was going to hang out around here in johto and wanted me to be her bodyguard. I know Blue, even if I denied she would have used any method to make me agree, and personally, I don't want to be in that situation ever again. I look at my Pokegear and see 2:35 pm, she's late. Of course, that's nothing different from what I'm used to. Heck, if it was that idiot Gold he would probably be about three hours late. I look down the street and see if she's approaching, only to see the girl with pink hair, Whitney.

"Hey Silver!" she calls out to me. Just ignore her Silver, and she'll probably go away… She calls out to me again, "Silver!" Just turn around, and start walking away…

"SILVER!" She screams as she runs up and tackles me. "Hey, what's the deal with ignoring me!"

"I'm looking for someone right now, I have no time for…" before I finish, I was interrupted by a gigantic explosion. It appeared to have been coming from the Goldenrod department store. Without another word, Whitney just made a mad dash to the department store. Seriously, didn't she think that this might be some sort of trap? Whatever, I'll go deal with it.

The Goldenrod department store, glowing brilliantly due to it's flames. I guess I never really looked too closely to notice, but it was a really awesome looking building. I rush through the crowd of people who are trying to escape the burning building, and I see no sign of Whitney. I look through the first floor, and nobody is there. I looked through the second floor, nobody was there. Finally, the third floor I could hear the Whitney's loud and slightly annoying voice. I decided to hide myself to understand the situation.

"Hey, what the heck is your problem!? Burning down this building, which is one of Johto's most important economic buildings!?" She stated. Maybe that was the point you idiot…

"We are here to take over the Johto Region, to create more water for the poor water pokemon. Seriously, with all of the land that is popping up everywhere, there won't be any room for the water pokemon. Don't you understand how sad that is?" A nameless grunt in blue clothing told her.

"I hate to disappoint you...But I am a gym leader of the Johto Region! You are not taking over as long as we gym leaders are here!"

"I see...So if the gym leaders are gone, then we can have the Johto Region? That sounds like a great idea! Seriously, the Johto region must not be worth much." The grunt said with the biggest clown smile(which was actually really creepy. Still, I guess I should start getting involved myself. I walked into the room, and then the three men instantly fell face first into the floor.

Both Whitney and I were completely confused by the situation, then I heard a voice I was hoping I wouldn't hear in this situation. The voice was laughing, as if it didn't even mind that the building was currently burning down. Only one person could be this nonchalant in this situation. It was Blue, I don't know how she did it, but she managed to take down a total of three grunts at almost seemingly the same time. Whitney runs out of the building after making sure it was empty and told me that she was going to warn the rest of the Johto gym leaders.

"So Silver, what exactly is going on here?" Blue asked, suddenly appearing behind me. I really hate it when she does that.

"Well, apparently some sort of organization is trying to take over the Johto region and sink it, so that there is more room for water pokemon to live. If you ask me, it's completely ridiculous."

"Huh, they're actually pretty smart..." Blue replied with a surprised voice.

"What do you mean?" I asked.

"Well, think about it. If they actually managed to take over Goldenrod they would be able to cut of the trade routes between the East and West of the Johto region. But, being in the center, that also leads room for more allied attacks against them. With minimal materials to prevent a war against them, there's just no way that this factor will have as much effect as it could."

So, these Lunatics in blue actually have a smart tactician. Interesting, I've been looking for a good challenge. Heck, this will keep me from being bored. Stopping a war before it starts, sounds like a challenge for the next heir of Team Rocket. This will be my first step in repairing my name as Giovanni's son.

**Sorry for those of you who have already read this part, but I felt like the story was missing a little bit of something. I hope you like it!**


	2. Chapter 1b: Rise of the Soldiers

Pokemon Special: Team Rocket's Last Stand

_Chapter 1b: The Rise of the Super Soldiers(Green POV)_

The gym door had been opened, hence the annoying bell that was currently ringing in my ears. I haven't had a challenger in a while, this might be interesting. The footsteps were flimsy, as if the man had forgotten to walk and I could hear heavy breathing. Meaning that whoever this was must be extremely injured, so I'll wait until he comes over here. At least, that's what I thought until I heard a scream coming from the other side of the gym. I rushed over to the scene, one of the trainers in my gym had been injured by a man in a Team Rocket Uniform.

"KILL... YOU'RE...NOT...TARGET…" The man had yelled.

"You'll pay for this!" I yelled as I charged at him.

"YOU! YESSSSS! TARGET!" In a few seconds, he closed the distance of about twenty feet and kicked me in the stomach. He had sent me flying to the back of the room, where I was previously located about two minutes ago.

"Damn, he's too strong. Machamp, hold him down!" I said before I started to vomit blood.

Once I looked again, the man had closed the distance between us and had attacked Machamp. Even Machamp had a hard time holding this man down. However, when it took advantage of having four arms we were able to hold the man. No matter who it was, no human has the power to fight Machamp in a one on one fight.

"DAMN! TARGET! MUST! KILL!" The man continued to scream.

"Tell me, whose orders are you following?" After I said this, a loud boom was heard from the gym entrance. A bullet had pierced the man's skull in mere moments.

"NOO...WHY...NOW…GROOOOAHHHH" Then, the annoying and powerful man had been slain. Before I was able to ask any questions, the man had been killed. I ran towards the entrance of the gym, but there was no one there. My Pokegear that I had received from Professor Oak began to ring, I was receiving a call from Yellow.

"...Hello? Yellow, what's up?' I answered in a serious voice, because it's not every day I receive a call from this kid. I'm hoping that she could shed a light on a few things.

"Green! You picked up! Thank goodness!" After this introduction she explained her situation to me.

Team Rocket has returned, and they captured Red. However, it seems that they are also able to give people these Superhuman Attributes. This is bad, I told Yellow that I would meet her in the Viridian Forest. I summoned Charizard and we began to fly towards Viridian Forest. I looked but was unable to find her, until I heard a boom and a large portion of the Viridian Forest had been destroyed.

"Let's go Charizard, head towards that crater!" I commanded, "I hope we're not too late."

I saw Yellow being pinned down by a mysterious force and a strangely colored Venusaur charging up an attack, so I told Charizard to attack the Venusaur. After the attack impacted, the Venusaur was instantly defeated. We headed down into the forest, only to hear some conversation between Yellow and the attacker.

"Damn, there's only one person who's capable of taking Venusaur down in one hit! This is bad, you lucked out this time kid!" After hearing this, it seemed that Yellow and her Kitty had been released from the enemies grasp.

We had finally landed on the forest ground, and Yellow had run over to the Venusaur. I asked for an explanation from her, but she told me that I had to wait. The Venusaur had stood up again, despite the heavy damage it had taken and was preparing an attack. It roared, not only a roar of pain, but it also sounded sad.

"Yellow, get back! Now!"

"No, I can't! Not until he wakes up from this nightmare!" She replied, and then closed her eyes. I remember that position, she's trying to read the mind of the Venusaur! She also seems to be healing it, why would she be healing the enemy? This doesn't make sense! The Venusaur continued to roar in pain the more Yellow continued to heal it. Could it be that Yellow knows something I don't?

Venusaur's attack was coming, and Yellow was completely defenseless. So I brought out my Golduck and Scizor, and ordered them to stop the Venusaur's attack. Yellow seems to know what she's doing, so I'm going to let her before the time being. If that means protecting her in enemy territory, then I will do just that. The strange color on the Venusaur began to fade away the more Yellow had healed it, so it seems that Yellow was right on the mark when deciding to heal this thing.

Finally, Yellow had finished to heal the beast. The Venusaur was at full health but it seemed to be exhausted. Yellow was out of it, as she had to use more power than usual. Still, it wouldn't be a bad idea to go to the Pokemon Center to let these two recover. So we got on Charizard, even though it was a bit tough for him and left back to head towards Viridian.

What we saw when we got there was a fiery inferno, everything was burnt down excluding the gym. Not a single person in sight, in the town. I hope they all got away safely. Damn, it hasn't even been five minutes since I left town! Who has the ability to do something like this!? If the enemy has grown so powerful, I can't beat them on my own. I'll contact every Pokedex Holder as reinforcements. Mark my word, you'll pay for this Team Rocket!


	3. Chapter 2a: A Legendary Problem

Pokemon Special: Team Rocket's Last Stand

_Chapter 2a: The Legendary Problem(Ruby POV)_

According to Green's call's, we immediately got onto the S.S Tidal and were immediately heading off to the Kanto region. The thing is that I received this call after I was spending some time conversing with Wallace. I told him that I wanted to do my best to avoid being seen by Sapphire, and he dressed me up to the point where I looked like a gangster, and he made me take off my lucky hat. Wallace and I were both on the deck, having ourselves a merry little time until I heard a scream that I could decipher from a mile away.

"Hide! She's here!" I exclaimed while hiding Wallace behind the dining table. Of course, she was heading over here. While I was panicking Wallace just stood up without the realization of what was going on.

"Well, if it isn't little Sapphire! How have you been?" Wallace introduced himself.

Sapphire cleared her throat, "Um, I have been, okay." she said surprisingly cleanly. A bit too cleanly, one might even question if it was her.

"You are much more fluent than you were before? What brought about the change?"

"I want to be with Ruby, and, english must improve. So that I, can be with him…" She said with a blush.

"You are so adorable, Sapphire! I am supporting you completely! Hey Rookie! How long are you going to be under the table?"

Damn, Wallace! Okay, I'm going to try playing this as smoothly as I possibly can. I have to trick Sapphire into thinking that I am not here.

"Yes sir Wallace! I was only checking to make sure that nobody had been hiding under the table. There was a report that somebody had been stealing food." Wait,WHAT? What the heck did I just say!? This must be the desperation of trying to get out of here, because I swear that I can come up with a better excuse than that!?

"Yes, just go make sure that none of the other guests are dissatisfied with their service. It is against this ship's policy to even have one dissatisfied customer! It's a long trip from Hoenn to Kanto, so make sure everybody is relaxed and comfortable!" Wallace replied.

"Wait a minute," The silent Emerald had finally spoken up, "That looked a lot like Ruby!"

"Non, non! Ruby is currently taking on new challengers at the Master Contest in Lilycove City! He has no time to be on a ship like this one!"

"What do you mean by that? I heard that this is serious! For Ruby not to be here at a time like this is just cruel!" Emerald yelled.

"I will try contacting him, so just cheer up! Also, tell me, what do you mean by 'at a time like this'?"

"Team Rocket, they're back. According to Green they've kidnapped a friend of ours, and they're creating these monsters that Green is calling Super Soldiers. Also, they used some kind of messed up technology to use the Friends pokemon for terrible things! Another of our friends was almost killed by it! If this isn't an emergency, then what is!?" Emerald cried out.

"Still as dire as the situation is, there is no need to be angry at your friend. If you take care of a friend, then he will take care of you just as much or even more. An ally is somebody who stands by you on a battlefield, but a friend will be with you wherever you go."

"If he's my friend, then where is he now? When we need him most?!"

"Emerald! You will stop now! No need to throw insults at Ruby any longer. He will come, he promised." Sapphire stopped Emerald with a smile.

Wallace walked over to me, "Sorry my friend, I may have accidentally made things worse…"

"No problem, he has every right to be mad. But, I just can't show my face to Sapphire yet. I'm not ready…"

Suddenly, the boat began to tilt. At first, it only managed to rock the boat but then we began to feel everything move to the side. We were caught in a gigantic net, and we were being pulled in by someone. Everybody was hanging on for dear life because the boat was almost overturned. The screams that filled the boat were loud as expected, but they demonstrated perfectly the fear that we were all experiencing.

"We have captured you all now! You will listen or we will destroy the ship along with everyone in it!" The man was on the enemy ship that had trapped us in the net. On his shirt, was a G. If my memories were working correctly, that's the G from Sinnoh's Team Galactic. But, what would a man from Sinnoh be doing in Hoenn waters, interfering with a boat that is supposed to be delivering materials?

"You can't stop us! Burn the net!" Sapphire had begun her attack, and her Blaziken had gone to attack the net. However, the net had not been broken. Sapphire continued to attack the net, but to no avail.

"You dare to defy Team Galactic?"

"You're in the way. That is all."

"I see, everyone commence the attack on the S.S Tidal. Make sure there are no survivors."

"I'm sorry everyone…" Sapphire had told herself.

"Please do not worry, Miss Sapphire. It will take more than a couple of Grunts to take _me _down!" Wallace told her. And thus the battle began, all of the passengers of the S.S Tidal. my self included, against Team Galactic.


	4. Chapter 2b: A Legendary Problem

Pokemon Special: Team Rocket's Last Stand

_Chapter 2a: The Legendary Problem(Pearl POV)_

According to the message we had received from Green, the orders were to go straight to Kanto to try and calm down the situation over there. He didn't really explain much, but he said something about super soldiers and dark pokemon. Is there really anyone in the world that possesses the power to control such things at will. No, there's no way that's possible, it's probably just an infection over at Kanto or something.

"Um, Pearl? Have you seen Missy anywhere?" Diamond asked.

"Are you serious?! You take your eyes off of her and she suddenly ends up getting lost!"

"Pearl, forget about that. I see fire…"

"We're in the middle of the ocean! There's no way there could be…" I said as I turned around. There were two boats, battling each other. One boat that we never heard of, and a boat that held the crest and flag of Team Galactic. From what I could tell, it seems that the boat with Team Galactics flag held the advantage. We began to approach the ship, and then we were able to see the people on board the unknown ship. The were wearing red clothes, imprinted with what appeared to be a mountain in their shirts.

"CHARGE! LONG LIVE TEAM MAGMA!" was heard throughout the entire ocean. The screams that followed came from the same people that charged at the Galactic Ship. They simply jumped overboard and swam towards the enemy ship. The battle continued, it seems as if they had overtaken the enemy!

"Pearl, who is Team Magma?" Diamond asked.

"I don't know Dia…" I replied, feeling powerless due to lack of knowledge.

"Team Magma, a secret organization that tried to expand Hoenn's land in exchange for losing the ocean. In attempt of this, they had summoned the legendary Groudon, and had almost destroyed the Hoenn Region in the process." We heard that familiar soft voice. It was Platinum. She was on top of our ship, and was staring off into the distance, as if she was amazed by the beauty of the destruction of the ship, and saddened because the ship had been destroyed.

Suddenly, a loud boom could be heard throughout the entire ship. We were not moving, everyone was silent. The more time that had passed by, the more we could feel that the ship was tilting. We're sinking!

"WE'RE ALL GONNA DIE!"

"WHY IS THE BOAT SINKING?"

"But I didn't get to go to the buffet yet…" Dia whined to himself.

"This is not the time to worry about something like that!" I said as I smacked Dia.

I looked around for Missy but she was nowhere to be found. What's going on? Why is the boat sinking? The answer then appeared right before my eyes.

"Lugia, another Aero Blast." we could hear this from the distance. A lone man was standing on top of the Lugia. He wore clothing as black as night, and his face was concealed with a mask that showed only the color of his eyes.

The boat was hit by the Aero Blast, and we began to sink faster. At this rate, the boat won't last five minutes. We have to get out of here! I try to reach out to Dia, but he disappeared. I called out for him, but there was no response. Don't tell me he's already fallen into the water…

"DIA! MISSY!" I exclaimed. No response, however when I looked up at the top of the ship which now was only about twenty feet above the water I saw the Masked Man and Missy.

"Listen Kid, you have two options, sink or come with me."

"I refuse to listen to a terrorist."

"I see, guess I have no choice then. Registeel, subdue her. Use Superpower." After I heard these words, I heard a scream. Then, I saw the masked man again. However this time he was holding Missy like a princess.

"Damn it, give her back!" I yelled.

"Lugia, Aero Blast." He said calmly. The boat had been destroyed, we were now trying to float on pieces of metal. After seeing that we were unable to fight back we heard him say this, "I have the girl. Yeah, I'm heading over to Saffron now." The man flew off on his Lugia and in about 3 seconds had disappeared from the horizon completely.

Wait, where's Dia!? I continuously called out to him, but got no response. Please, you can't tell me he's drowned. I haven't been able to do anything! Why am I so useless! The Ship that was being attacked by Team Galactic was appearing to head over here. Dang it, is this a part of their trap too?

When the ship had finally reached us, it sent out rescue boats in an attempt to rescue us. They were surprisingly kinder than I thought they were. seeing as they also gave us blankets to warm up from the cold water. It's surprising, but I can't let my guard down. I have to remember that these guys almost destroyed that Hoenn region.

"Hello, are you Sir Pearl? We were hoping that we would've been able to meet under more normal conditions but it seems as if the plan has changed. Please head over to the Captain's office and we will head over there ourselves as soon as we have this situation under control." He said to me in a military like voice.

I start to head over to the Captain's office and find the one guy who helped brighten up my day. Dia was alive! and eating a bunch of food. I'll forgive him this one time because things couldn't be worse right now. We had finally arrived to the Captain's Office to find three people in here already. I'd seen pictures of two of them, it was Sapphire and Emerald. Two of the Hoenn Pokedex users! However, we had no conversations going on, as they had a rather serious look on their face.

"Hello, I am a lowly messenger from Team Magma. I've come to tell you a message from the Higher Ups. We of Team Magma have signed a treaty with Team Rocket, and are going to war against Team Galactic. This was known as the Rocket Magma army. Team Galactic has currently recruited Team Aqua into their ranks. We were told to leave the Pokedex users out of our violence."

Wait, what? If they were told to leave us out of it, then why did Team Rocket capture Red? Harm Yellow? Attempt to take the life of Green? This doesn't make any sense! Why would they do something like this?

"What's the deal with the Supersoldiers?" I asked.

"That's Confidential Information."

"The Black Venusaur?"

"Also Confidential."

"Red's Kidnapping?'

"..."

"Damn it, if you won't tell us anything then you are the enemy! I won't sit here as you start hurting my friends!"

"I understand where you're coming from. However, rushing things will get us nowhere. We were told to drop you off near Saffron, and that is what we are going to do. Enjoy the rest of the boat ride."

The Man in the red coat left, leaving nothing but silence in the room. In the end, we learned nothing about Team Rocket or their motives. I had a conversation with the Hoenn Dex Holders about the situation and we began to compare information.


End file.
